diffpy.structure 3.3.1rc0__tar.gz → 3.4.0rc0__tar.gz

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: diffpy.structure
-Version: 3.3.1rc0
+Version: 3.4.0rc0
 Summary: Crystal structure container and parsers for structure formats.
-Author-email: Simon Billinge <sb2896@columbia.edu>
-Maintainer-email: Simon Billinge <sb2896@columbia.edu>
+Author-email: Simon Billinge <sbillinge@ucsb.edu>
+Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
 Project-URL: Homepage, https://github.com/diffpy/diffpy.structure/
 Project-URL: Issues, https://github.com/diffpy/diffpy.structure/issues/
 Keywords: diffpy,crystal structure data storage,CIF,PDB
@@ -16,12 +16,12 @@ Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: <3.14,>=3.11
+Requires-Python: <3.15,>=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE-DANSE.rst
 License-File: LICENSE-pymmlib.rst
@@ -29,6 +29,7 @@ License-File: LICENSE.rst
 License-File: AUTHORS.rst
 Requires-Dist: numpy
 Requires-Dist: pycifrw
+Requires-Dist: diffpy.utils
 Dynamic: license-file
 
 |Icon| |title|_
@@ -58,6 +59,7 @@ Dynamic: license-file
         :target: https://anaconda.org/conda-forge/diffpy.structure
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.structure/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.structure
         :target: https://pypi.org/project/diffpy.structure/
@@ -132,6 +134,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.structure --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.structure -h
+
 Getting Started
 ---------------
 
@@ -167,8 +182,15 @@ Improvements and fixes are always appreciated.
 
 Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
-Acknowledgement
----------------
+Contact
+-------
+
+For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainer``Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
 
 Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
 originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
@@ -177,8 +199,3 @@ Less common settings of space groups were generating using the
 `Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
 
 ``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
-
-Contact
--------
-
-For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/README.rst

@@ -25,6 +25,7 @@
         :target: https://anaconda.org/conda-forge/diffpy.structure
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.structure/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.structure
         :target: https://pypi.org/project/diffpy.structure/
@@ -99,6 +100,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.structure --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.structure; print(diffpy.structure.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.structure -h
+
 Getting Started
 ---------------
 
@@ -134,8 +148,15 @@ Improvements and fixes are always appreciated.
 
 Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
-Acknowledgement
----------------
+Contact
+-------
+
+For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainer``Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
 
 Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
 originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
@@ -144,8 +165,3 @@ Less common settings of space groups were generating using the
 `Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
 
 ``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
-
-Contact
--------
-
-For more information on diffpy.structure please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at sb2896@columbia.edu.

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/pyproject.toml

@@ -6,15 +6,15 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.structure"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon Billinge", email="sb2896@columbia.edu" },
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 maintainers = [
-  { name="Simon Billinge", email="sb2896@columbia.edu" },
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 description = "Crystal structure container and parsers for structure formats."
 keywords = ['diffpy', 'crystal structure data storage', 'CIF', 'PDB']
 readme = "README.rst"
-requires-python = ">=3.11, <3.14"
+requires-python = ">=3.12, <3.15"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,16 +25,13 @@ classifiers = [
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
+        'Programming Language :: Python :: 3.14',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
 
-[project.scripts]
-transtru = "diffpy.structure.apps.transtru:main"
-
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.structure/"
 Issues = "https://github.com/diffpy/diffpy.structure/issues/"
@@ -51,6 +48,9 @@ include = ["*"]  # package names should match these glob patterns (["*"] by defa
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[project.scripts]
+diffpy-structure = "diffpy.structure.app:main"
+
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/requirements/conda.txt

@@ -1,2 +1,3 @@
 numpy
 pycifrw
+diffpy.utils

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/requirements/docs.txt

@@ -2,4 +2,4 @@ sphinx
 sphinx_rtd_theme
 sphinx-copybutton
 doctr
-m2r
+m2r2

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/requirements/pip.txt

@@ -1,2 +1,3 @@
 numpy
 pycifrw
+diffpy.utils

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2026 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2026 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Chris Farrow, Pavol Juhas,  Simon Billinge, Billinge Group members.
@@ -33,8 +33,10 @@ Exceptions:
     * SymmetryError
 """
 
-# Interface definitions ------------------------------------------------------
 
+import sys
+
+import diffpy.structure as _structure
 from diffpy.structure.atom import Atom
 from diffpy.structure.lattice import Lattice
 from diffpy.structure.parsers import getParser
@@ -45,6 +47,28 @@ from diffpy.structure.structureerrors import LatticeError, StructureFormatError,
 # package version
 from diffpy.structure.version import __version__
 
+# Deprecations -------------------------------------------------------
+
+
+# @deprecated
+# custom deprecator for diffpy.Structure module
+class DeprecatedStructureModule:
+    """Proxy for backward compatibility of diffpy.Structure."""
+
+    def __getattr__(self, name):
+        import warnings
+
+        warnings.warn(
+            "Module 'diffpy.Structure' is deprecated and will be removed in version 4.0. "
+            "Use 'diffpy.structure' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return getattr(_structure, name)
+
+
+sys.modules["diffpy.Structure"] = DeprecatedStructureModule()
+
 # top level routines
 
 

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/_legacy_importer.py

@@ -80,7 +80,11 @@ class MapRenamedStructureModule(importlib.abc.Loader):
 # ----------------------------------------------------------------------------
 
 # show deprecation warning for diffpy.Structure
-warn(WMSG.format("diffpy.Structure", "diffpy.structure"), DeprecationWarning, stacklevel=2)
+warn(
+    WMSG.format("diffpy.Structure", "diffpy.structure"),
+    DeprecationWarning,
+    stacklevel=2,
+)
 
 # install meta path finder for diffpy.Structure submodules
 sys.meta_path.append(FindRenamedStructureModule())

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/apps/anyeye.py

@@ -138,7 +138,10 @@ def convertStructureFile(pd):
     if pd["formula"]:
         formula = pd["formula"]
         if len(formula) != len(stru):
-            emsg = "Formula has %i atoms while structure %i" % (len(formula), len(stru))
+            emsg = "Formula has %i atoms while structure %i" % (
+                len(formula),
+                len(stru),
+            )
             raise RuntimeError(emsg)
         for a, el in zip(stru, formula):
             a.element = el
@@ -217,7 +220,9 @@ def main():
     pd["watch"] = False
     try:
         opts, args = getopt.getopt(
-            sys.argv[1:], "f:whV", ["formula=", "watch", "viewer=", "formats=", "help", "version"]
+            sys.argv[1:],
+            "f:whV",
+            ["formula=", "watch", "viewer=", "formats=", "help", "version"],
         )
     except getopt.GetoptError as errmsg:
         print(errmsg, file=sys.stderr)

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/apps/transtru.py

@@ -99,7 +99,10 @@ def main():
             print("'%s' is not valid output format" % outfmt, file=sys.stderr)
             sys.exit(2)
     except ValueError:
-        print("invalid format specification '%s' does not contain .." % args[0], file=sys.stderr)
+        print(
+            "invalid format specification '%s' does not contain .." % args[0],
+            file=sys.stderr,
+        )
         sys.exit(2)
     # ready to do some real work
     try:

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/atom.py

@@ -201,7 +201,13 @@ class Atom(object):
     def __repr__(self):
         """String representation of this Atom."""
         xyz = self.xyz
-        s = "%-4s %8.6f %8.6f %8.6f %6.4f" % (self.element, xyz[0], xyz[1], xyz[2], self.occupancy)
+        s = "%-4s %8.6f %8.6f %8.6f %6.4f" % (
+            self.element,
+            xyz[0],
+            xyz[1],
+            xyz[2],
+            self.occupancy,
+        )
         return s
 
     def __copy__(self, target=None):
@@ -355,13 +361,19 @@ class Atom(object):
         """
 
     U11 = property(
-        lambda self: self._get_Uij(0, 0), lambda self, value: self._set_Uij(0, 0, value), doc=_doc_uii.format(0)
+        lambda self: self._get_Uij(0, 0),
+        lambda self, value: self._set_Uij(0, 0, value),
+        doc=_doc_uii.format(0),
     )
     U22 = property(
-        lambda self: self._get_Uij(1, 1), lambda self, value: self._set_Uij(1, 1, value), doc=_doc_uii.format(1)
+        lambda self: self._get_Uij(1, 1),
+        lambda self, value: self._set_Uij(1, 1, value),
+        doc=_doc_uii.format(1),
     )
     U33 = property(
-        lambda self: self._get_Uij(2, 2), lambda self, value: self._set_Uij(2, 2, value), doc=_doc_uii.format(2)
+        lambda self: self._get_Uij(2, 2),
+        lambda self, value: self._set_Uij(2, 2, value),
+        doc=_doc_uii.format(2),
     )
 
     _doc_uij = """
@@ -372,13 +384,19 @@ class Atom(object):
         """
 
     U12 = property(
-        lambda self: self._get_Uij(0, 1), lambda self, value: self._set_Uij(0, 1, value), doc=_doc_uij.format(0, 1)
+        lambda self: self._get_Uij(0, 1),
+        lambda self, value: self._set_Uij(0, 1, value),
+        doc=_doc_uij.format(0, 1),
     )
     U13 = property(
-        lambda self: self._get_Uij(0, 2), lambda self, value: self._set_Uij(0, 2, value), doc=_doc_uij.format(0, 2)
+        lambda self: self._get_Uij(0, 2),
+        lambda self, value: self._set_Uij(0, 2, value),
+        doc=_doc_uij.format(0, 2),
     )
     U23 = property(
-        lambda self: self._get_Uij(1, 2), lambda self, value: self._set_Uij(1, 2, value), doc=_doc_uij.format(1, 2)
+        lambda self: self._get_Uij(1, 2),
+        lambda self, value: self._set_Uij(1, 2, value),
+        doc=_doc_uij.format(1, 2),
     )
 
     # clean local variables

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/lattice.py

@@ -31,7 +31,16 @@ from diffpy.structure.structureerrors import LatticeError
 # Helper Functions -----------------------------------------------------------
 
 # exact values of cosd
-_EXACT_COSD = {0.0: +1.0, 60.0: +0.5, 90.0: 0.0, 120.0: -0.5, 180.0: -1.0, 240.0: -0.5, 270.0: 0.0, 300.0: +0.5}
+_EXACT_COSD = {
+    0.0: +1.0,
+    60.0: +0.5,
+    90.0: 0.0,
+    120.0: -0.5,
+    180.0: -1.0,
+    240.0: -0.5,
+    270.0: 0.0,
+    300.0: +0.5,
+}
 
 
 def cosd(x):
@@ -158,15 +167,21 @@ class Lattice(object):
     # properties -------------------------------------------------------------
 
     a = property(
-        lambda self: self._a, lambda self, value: self.setLatPar(a=value), doc="The unit cell length *a*."
+        lambda self: self._a,
+        lambda self, value: self.setLatPar(a=value),
+        doc="The unit cell length *a*.",
     )
 
     b = property(
-        lambda self: self._b, lambda self, value: self.setLatPar(b=value), doc="The unit cell length *b*."
+        lambda self: self._b,
+        lambda self, value: self.setLatPar(b=value),
+        doc="The unit cell length *b*.",
     )
 
     c = property(
-        lambda self: self._c, lambda self, value: self.setLatPar(c=value), doc="The unit cell length *c*."
+        lambda self: self._c,
+        lambda self, value: self.setLatPar(c=value),
+        doc="The unit cell length *c*.",
     )
 
     alpha = property(
@@ -200,19 +215,40 @@ class Lattice(object):
         rv = math.sqrt(1.0 + 2.0 * ca * cb * cg - ca * ca - cb * cb - cg * cg)
         return rv
 
-    volume = property(lambda self: self.a * self.b * self.c * self.unitvolume, doc="The unit cell volume.")
+    volume = property(
+        lambda self: self.a * self.b * self.c * self.unitvolume,
+        doc="The unit cell volume.",
+    )
 
-    ar = property(lambda self: self._ar, doc="The cell length *a* of the reciprocal lattice.")
+    ar = property(
+        lambda self: self._ar,
+        doc="The cell length *a* of the reciprocal lattice.",
+    )
 
-    br = property(lambda self: self._br, doc="The cell length *b* of the reciprocal lattice.")
+    br = property(
+        lambda self: self._br,
+        doc="The cell length *b* of the reciprocal lattice.",
+    )
 
-    cr = property(lambda self: self._cr, doc="The cell length *c* of the reciprocal lattice.")
+    cr = property(
+        lambda self: self._cr,
+        doc="The cell length *c* of the reciprocal lattice.",
+    )
 
-    alphar = property(lambda self: self._alphar, doc="The reciprocal cell angle *alpha* in degrees.")
+    alphar = property(
+        lambda self: self._alphar,
+        doc="The reciprocal cell angle *alpha* in degrees.",
+    )
 
-    betar = property(lambda self: self._betar, doc="The reciprocal cell angle *beta* in degrees")
+    betar = property(
+        lambda self: self._betar,
+        doc="The reciprocal cell angle *beta* in degrees",
+    )
 
-    gammar = property(lambda self: self._gammar, doc="The reciprocal cell angle *gamma* in degrees")
+    gammar = property(
+        lambda self: self._gammar,
+        doc="The reciprocal cell angle *gamma* in degrees",
+    )
 
     ca = property(lambda self: self._ca, doc="The cosine of the cell angle *alpha*.")
 
@@ -226,11 +262,20 @@ class Lattice(object):
 
     sg = property(lambda self: self._sg, doc="The sine of the cell angle *gamma*.")
 
-    car = property(lambda self: self._car, doc="The cosine of the reciprocal angle *alpha*.")
+    car = property(
+        lambda self: self._car,
+        doc="The cosine of the reciprocal angle *alpha*.",
+    )
 
-    cbr = property(lambda self: self._cbr, doc="The cosine of the reciprocal angle *beta*.")
+    cbr = property(
+        lambda self: self._cbr,
+        doc="The cosine of the reciprocal angle *beta*.",
+    )
 
-    cgr = property(lambda self: self._cgr, doc="The cosine of the reciprocal angle *gamma*.")
+    cgr = property(
+        lambda self: self._cgr,
+        doc="The cosine of the reciprocal angle *gamma*.",
+    )
 
     sar = property(lambda self: self._sar, doc="The sine of the reciprocal angle *alpha*.")
 
@@ -240,7 +285,17 @@ class Lattice(object):
 
     # done with properties ---------------------------------------------------
 
-    def __init__(self, a=None, b=None, c=None, alpha=None, beta=None, gamma=None, baserot=None, base=None):
+    def __init__(
+        self,
+        a=None,
+        b=None,
+        c=None,
+        alpha=None,
+        beta=None,
+        gamma=None,
+        baserot=None,
+        base=None,
+    ):
         # build a set of provided argument names for later use.
         apairs = (
             ("a", a),
@@ -287,7 +342,16 @@ class Lattice(object):
             self.setLatPar(a, b, c, alpha, beta, gamma, baserot=baserot)
         return
 
-    def setLatPar(self, a=None, b=None, c=None, alpha=None, beta=None, gamma=None, baserot=None):
+    def setLatPar(
+        self,
+        a=None,
+        b=None,
+        c=None,
+        alpha=None,
+        beta=None,
+        gamma=None,
+        baserot=None,
+    ):
         """Set one or more lattice parameters.
 
         This updates all attributes that depend on the lattice parameters.
@@ -361,7 +425,11 @@ class Lattice(object):
         )
         # standard Cartesian coordinates of lattice vectors
         self.stdbase = numpy.array(
-            [[1.0 / ar, -cgr / sgr / ar, cb * self.a], [0.0, self.b * sa, self.b * ca], [0.0, 0.0, self.c]],
+            [
+                [1.0 / ar, -cgr / sgr / ar, cb * self.a],
+                [0.0, self.b * sa, self.b * ca],
+                [0.0, 0.0, self.c],
+            ],
             dtype=float,
         )
         # Cartesian coordinates of lattice vectors
@@ -423,7 +491,12 @@ class Lattice(object):
         self._gammar = math.degrees(math.acos(cgr))
         # standard orientation of lattice vectors
         self.stdbase = numpy.array(
-            [[1.0 / ar, -cgr / sgr / ar, cb * a], [0.0, b * sa, b * ca], [0.0, 0.0, c]], dtype=float
+            [
+                [1.0 / ar, -cgr / sgr / ar, cb * a],
+                [0.0, b * sa, b * ca],
+                [0.0, 0.0, c],
+            ],
+            dtype=float,
         )
         # calculate unit cell rotation matrix, base = stdbase @ baserot
         self.baserot = numpy.dot(numalg.inv(self.stdbase), self.base)
@@ -434,7 +507,11 @@ class Lattice(object):
         self.isotropicunit = _isotropicunit(self.recnormbase)
         # update metrics tensor
         self.metrics = numpy.array(
-            [[a * a, a * b * cg, a * c * cb], [b * a * cg, b * b, b * c * ca], [c * a * cb, c * b * ca, c * c]],
+            [
+                [a * a, a * b * cg, a * c * cb],
+                [b * a * cg, b * b, b * c * ca],
+                [c * a * cb, c * b * ca, c * c],
+            ],
             dtype=float,
         )
         return

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/mmlibspacegroups.py

@@ -3269,7 +3269,11 @@ sg143 = SpaceGroup(
     point_group_name="PG3",
     crystal_system="TRIGONAL",
     pdb_name="P 3",
-    symop_list=[SymOp(Rot_X_Y_Z, Tr_0_0_0), SymOp(Rot_mY_XmY_Z, Tr_0_0_0), SymOp(Rot_mXY_mX_Z, Tr_0_0_0)],
+    symop_list=[
+        SymOp(Rot_X_Y_Z, Tr_0_0_0),
+        SymOp(Rot_mY_XmY_Z, Tr_0_0_0),
+        SymOp(Rot_mXY_mX_Z, Tr_0_0_0),
+    ],
 )
 
 sg144 = SpaceGroup(
@@ -3280,7 +3284,11 @@ sg144 = SpaceGroup(
     point_group_name="PG3",
     crystal_system="TRIGONAL",
     pdb_name="P 31",
-    symop_list=[SymOp(Rot_X_Y_Z, Tr_0_0_0), SymOp(Rot_mY_XmY_Z, Tr_0_0_13), SymOp(Rot_mXY_mX_Z, Tr_0_0_23)],
+    symop_list=[
+        SymOp(Rot_X_Y_Z, Tr_0_0_0),
+        SymOp(Rot_mY_XmY_Z, Tr_0_0_13),
+        SymOp(Rot_mXY_mX_Z, Tr_0_0_23),
+    ],
 )
 
 sg145 = SpaceGroup(
@@ -3291,7 +3299,11 @@ sg145 = SpaceGroup(
     point_group_name="PG3",
     crystal_system="TRIGONAL",
     pdb_name="P 32",
-    symop_list=[SymOp(Rot_X_Y_Z, Tr_0_0_0), SymOp(Rot_mY_XmY_Z, Tr_0_0_23), SymOp(Rot_mXY_mX_Z, Tr_0_0_13)],
+    symop_list=[
+        SymOp(Rot_X_Y_Z, Tr_0_0_0),
+        SymOp(Rot_mY_XmY_Z, Tr_0_0_23),
+        SymOp(Rot_mXY_mX_Z, Tr_0_0_13),
+    ],
 )
 
 sg146 = SpaceGroup(
@@ -3323,7 +3335,11 @@ sg1146 = SpaceGroup(
     point_group_name="PG3",
     crystal_system="TRIGONAL",
     pdb_name="R 3",
-    symop_list=[SymOp(Rot_X_Y_Z, Tr_0_0_0), SymOp(Rot_Z_X_Y, Tr_0_0_0), SymOp(Rot_Y_Z_X, Tr_0_0_0)],
+    symop_list=[
+        SymOp(Rot_X_Y_Z, Tr_0_0_0),
+        SymOp(Rot_Z_X_Y, Tr_0_0_0),
+        SymOp(Rot_Y_Z_X, Tr_0_0_0),
+    ],
 )
 
 sg147 = SpaceGroup(

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/parsers/p_auto.py

@@ -190,7 +190,10 @@ class P_auto(StructureParser):
                 pass
         if stru is None:
             emsg = "\n".join(
-                ["Unknown or invalid structure format.", "Errors per each tested structure format:"]
+                [
+                    "Unknown or invalid structure format.",
+                    "Errors per each tested structure format:",
+                ]
                 + parsers_emsgs
             )
             raise StructureFormatError(emsg)

{diffpy_structure-3.3.1rc0 → diffpy_structure-3.4.0rc0}/src/diffpy/structure/parsers/p_cif.py

@@ -32,6 +32,7 @@ import sys
 from contextlib import contextmanager
 
 import numpy
+from CifFile.yapps3_compiled_rt import YappsSyntaxError
 
 from diffpy.structure import Atom, Lattice, Structure
 from diffpy.structure.parsers import StructureParser
@@ -408,7 +409,7 @@ class P_cif(StructureParser):
                     # stop after reading the first structure
                     if self.stru is not None:
                         break
-        except (StarError, ValueError, IndexError) as err:
+        except (YappsSyntaxError, StarError, ValueError, IndexError) as err:
             exc_type, exc_value, exc_traceback = sys.exc_info()
             emsg = str(err).strip()
             e = StructureFormatError(emsg)
@@ -553,7 +554,10 @@ class P_cif(StructureParser):
         from diffpy.structure.spacegroups import FindSpaceGroup, GetSpaceGroup, IsSpaceGroupIdentifier, SpaceGroup
 
         self.asymmetric_unit = list(self.stru)
-        sym_synonyms = ("_space_group_symop_operation_xyz", "_symmetry_equiv_pos_as_xyz")
+        sym_synonyms = (
+            "_space_group_symop_operation_xyz",
+            "_symmetry_equiv_pos_as_xyz",
+        )
         sym_loop_name = [n for n in sym_synonyms if n in block]
         # recover explicit list of symmetry operations
         symop_list = []
@@ -591,7 +595,9 @@ class P_cif(StructureParser):
                 block.get("_space_group_crystal_system") or block.get("_symmetry_cell_setting") or "TRICLINIC"
             ).upper()
             self.spacegroup = SpaceGroup(
-                short_name=new_short_name, crystal_system=new_crystal_system, symop_list=symop_list
+                short_name=new_short_name,
+                crystal_system=new_crystal_system,
+                symop_list=symop_list,
             )
         if self.spacegroup is None:
             emsg = "CIF file has unknown space group identifier {!r}."